Amino Acids and Proteins Flashcards
What is meant by all amino acids are amphoteric?
They have the ability to act as acids and bases in reactions.
pKa of carboxyl and amino groups
carboxyl = 2
amino groups = 10
When the pH of the solution is less than the pKa of an acidic group, the acidic group will be mostly__
When the pH of the solution is less than the pKa of an acidic group, the acidic group will be mostly in its protonated form
When the pH of the solution is greater than the pKa of an acidic group, the acidic group will be mostly____
When the pH of the solution is greater than the pKa of an acidic group, the acidic group will be mostly in its deprotonated form
henderson hasselbalch equation
calculating pI of a molcule (i.e. AA) with 2 functional groups
average the pKa’s of the two functional groups
How to compare the pH of a solution to the pKa of the functional group of an AA and determine if a site is mostly protonated or deprotonated?
If the pH is higher than the pKa, the site is mostly deprotonated; if the pH is lower than the pKa, the site is mostly protonated
How are polypeptides linked together
Peptide bond - b/w the carboxyl group of one AA and the α-amino group of the another AA
polypeptide backbone formation
N-C-C-N-C-C
How do we break apart proteins?
Via Hydrolysis, by another protein called a proteolysis or proteolytic cleavage and the enzyme is called a protease
Primary protein structure
AA sequence
Secondary structure
H-bonding between the backbone groups (NH and CO)
Tertiary Structure
folding due to side chain interactions within a polypeptide
types of interactions in Tertiary Structure
Noncovalent
- acid/base (electrostatic)
- polar/polar
- nonpolar/nonpolar
Covalent
- disulfide bridges (b/w cysteine)
Quaternary Structure
side-chain inreractions between different polypeptides.
NOT all proteins have this structure
How do we drive endergonic reactions forward?
couple it with exergonic reactions
Hydrolase
hydrolyzes chemical bonds (including ATPases, proteases, and others)
Isomerase
rearranges bonds within a molcule to form an isomer (i.e. second half of PPP)
Ligase
forms a chemical bond (e.g., DNA ligase)
Lyase
breaks chemical bonds by means other than oxidation or hydrolysis (e.g., pyruvate decarboxylase)
Kinase
transfers a phosphate group to a molcule from a high energy carrier, such as ATP (e.g., phosphofructokinase [PFK])
Oxioreductase (give examples as well)
runs redox reactions (includes oxidaes, reductases, dehydrogenases, and others)
Polymerase
polymerization (e.g. addition of nucleotides to the leading strong of DNA by DNA polymerase III)
Phosphatase
removes a phosphate group from a molecule
Phosphorylase
transphers a phosphate group to a molecule from inorganic phosphate (e.g., glycogen phosphorylase)
Protease
hydrolizes peptide bonds (e.g., trypsin, chymotrypsin, pepsin, etc.)
Cofactors
metal ions or small molecules (not themselves a protein) that are required for activity in many enzymes. Vitamins in our diet serve as precursors for cofactors
coenzymes
when a cofactor is an organic molecule
What is Km?
Km is the concentration of substrate [S] required to reach 1/2 Vmax
explain affinity and Km
It is like an affinity the enzyme has for the substrate and has an inverse relationship.
Increase affinity = decreased Km (less substrate needed to reach Km)
What is meant by Vmax what does it depend on?
Vmax is the maximum rate of product formation, when the enzymes are completely saturated by substrate
- Depends on:*
- enzymes you have
- enzyme concentration
- NOT impacted by substrate
Competitive Inhibition
- binds at: active site
- effect on Vmax: No effect (can be overcome by addition of more substrate)
- e_ffect on Km_: Increased (meaning decreased affinity since there are others competing now)
Non-Competitive Inhibitors
- binds at: allosteric site (turn enzymes off)
- effect on Vmax: decreases (some enzymes are turned off thus less product formation)
- effect on Km: Unchanged (binds at allosteric site, thus doesn’t affect substrate binding)
Un-competitive Inhibitors
- binds at: allosteric site of ES compelx (after substrate binds)
- e_ffect on Vmax:_ decreases (some enzymes inactivated, less product formed)
- effect on Km: decreases (greater affinity since the substrate gets locked in)
Mixed Inhibitors
- binds at: allosteric site of ES compelx (after substrate binds) OR allosteric site on E alone (Δ shape of active site)
- effect on Vmax: decreases (since mimic uncom or noncom)
- effect on Km: increased, decreased, or unchanged (need to know more about inhibitor)
Describe Key components of Lineweaver-Burk Plots
Inverse Plots: 1/V vs. 1/[S]
V = rate of product formation
[S] = concentration of substrate
y-intercept: 1/Vmax
x-intercept: -1/Km
As you approach interssection point on the graph, the denominator is getting bigger
Type of Inhibitors in these graphs:
Monomers of Carbohydrates and formula
Carbohydrates CnH2nOn
common monosaccharides
6 Carbon Sugars
glucose
fructose
galactose
5 Carbon Sugars
ribose
deoxyribose
Most common disaccharides and their constituent components
For the MCAT, they will all be something plus glucose
1) Maltose - glucose + glucose
2) Sucrose - glucose + fructose
3) Lactose = glucose + galactose
3 most common and their function
Glycogen: animal glucose storage
Starch: plant glucose storage
Cellulose: plant structure (humans can’t digest)
Functions of Carbohydrates
- Energy
- cells preferred energy storage
- think reduction of glucose via cellular respiration
- Cell surface markers
- distinguishes b/w different types of cells (liver vs. muscle)
- adhesion
- carbs are sticky
Monomers of lipids
hydrocarbons
